Target Functional Analysis

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1 BioVLAB-MMIA-NGS BioVLAB-MMIA-NGS is Cloud-based miRNA mRNA integraed analysis system using NGS data. System computes differentially/significantly expressed miRNAs (DEmiRNAs) and mRNAs/genes (DEGs), and with targeting information, DEGs targeted by DEmiRNAs and having negative correlation between them are extracted. /
  • human
  • mice
  • macaca
  • plants (rice)
  • GO Terms
  • KEGG Pathways
  • miRNA/mRNA Correlation
  • Homepage

    Publication
    Sept. 29, 2014
    Citations: 5
    2 BUFET BUFET (Bitset-based Unbiased Functional Enrichment Tool) is a tool that performs the unbiased miRNA functional enrichment analysis (Bleazard et al.) requiring significantly reduced execution times (less than 10 minutes for 1 million random permutations). Users can provide their own interaction and annotation data in CSV files, making it a flexible tool for miRNA functional enrichment analysis. /
  • any
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    Sept. 6, 2017
    Citations: 0
    3 CPSS CPSS is (a computational platform for the analysis of small RNA deep sequencing data), designed to completely annotate and functionally analyse microRNAs (miRNAs) from NGS data on one platform with a single data submission. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • other animals (selectable)
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • Homepage

    Publication
    May 9, 2012
    Citations: 17
    4 DeAnnIso DeAnnIso, is an online tool, that is designed for Detection and Annotation of IsomiR from small RNA sequencing data. The detected isomiRs will be classified into different categories. The isomiRs will be aligned with canonical miRNA, and will be annotated with expression, constitution, SNP, and an in-house dataset. It can also extract differentially expressing isomiR between two samples. In addition, IsomiR Bank provides targets prediction and enrichment analysis to evaluate the effects of isomiRs on target selection. /
  • human
  • mouse
  • fish
  • fly
  • plants (selectable)
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    May 13, 2016
    Citations: 5
    5 DIANA-microT-CDS DIANA-microT-CDS is the 5th version of the microT algorithm. It is specifically trained on a positive and a negative set of miRNA Recognition Elements (MREs) located in both the 3'-UTR and CDS regions. DIANA-microT-CDS provides a significant increase in sensitivity compared to the previous version (65% vs 52%), when compared against experimental proteomics data. /
  • human
  • mouse
  • fly
  • worm
  • Literature Mining
  • Homepage

    Publication
    May 16, 2013
    Citations: 170
    6 DIANA-mirPath v3 DIANA-mirPath is a miRNA pathway analysis web-server, providing accurate statistics, while being able to accommodate advanced pipelines. mirPath can utilize predicted miRNA targets (in CDS or 3’-UTR regions) provided by the DIANA-microT-CDS algorithm or even experimentally validated miRNA interactions derived from DIANA-TarBase. These interactions (predicted and/or validated) can be subsequently combined with sophisticated merging and meta-analysis algorithms. /
  • human
  • mouse
  • fly
  • worm
  • rat
  • fish
  • chicken
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    May 14, 2015
    Citations: 156
    7 ElMMo3 A Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and assigns a posterior probability to each putative target site. /
  • human
  • mouse
  • rat
  • fish
  • fly
  • worm
  • GO Terms
  • Homepage

    Publication
    March 1, 2007
    Citations: 135
    8 Empirical GO The Empirical GO algorithm is a Python script that generates the empirical distribution of the number of microRNA target genes in GO terms and returns p-values for enrichment. /
  • any (from miRBase)
  • GO Terms
  • Homepage

    Publication
    Jan. 20, 2015
    Citations: 32
    9 IntaRNA IntaRNA is a program for the fast and accurate prediction of interactions between two RNA molecules. It has been designed to predict mRNA target sites for given non-coding RNAs (ncRNAs) like eukaryotic microRNAs (miRNAs) or bacterial small RNAs (sRNAs), but it can also be used to predict other types of RNA-RNA interactions. /
  • any
  • GO Terms
  • Homepage

    Publication
    Oct. 21, 2008
    Citations: 146
    10 isomiR2Function somiR2Function allows for the high-throughput detection of plant isomiRs from any miRNA-seq profiling study. isomiR2Function not only allows for the identification of the templated and non-templated 5′- isomiRs and 3′- isomiRs but also allows for the expression quantification. Since, the prediction of biologically relevant target is an important criterion for the identification of isomiRs and their targets - isomiR2Function identifies target as well. Following target prediction, it allows for functional enrichment of the identified targets. In parallel, isomiR2Function provides support for the visualization of read mapping on corresponding precursor sequences. /
  • plants
  • GO Terms
  • Homepage

    Publication
    March 21, 2017
    Citations: 0
    11 MAGI MAGI is a web service for fast MicroRNA-Seq data analysis in a graphics processing unit (GPU) infrastructure. Using just a browser, users have access to results as web reports in just a few hours—>600% end-to-end performance improvement over state of the art. /
  • human
  • KEGG Pathways
  • Homepage

    Publication
    June 6, 2014
    Citations: 7
    12 MAGIA2 MAGIA2 refines in silico target prediction through miRNA–target expression association measures. MAGIA2 extends the analysis, supporting multiple organisms (human, mouse, rat and drosophila), and using a greatly expanded list of target predictions algorithms. /
  • human
  • mouse
  • rat
  • fly
  • GO Terms
  • KEGG Pathways
  • miRNA/mRNA Correlation
  • Protein-Protein Interaction
  • Homepage

    Publication
    May 21, 2012
    Citations: 40
    13 miR2GO miR2GO is a web-based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO and miRpair2GO. miRmut2GO implements a knowledge-based method to assess the functional effects of genetic and somatic mutations in microRNA seed regions. The functional effects of a mutation are analysed by semantic comparison of enriched gene ontology (GO) annotations of the target gene sets for the wild-type and mutated alleles. miRpair2GO compares the functions of two different miRNAs based on the enriched functional annotations of their target gene sets. /
  • human
  • GO Terms
  • Homepage

    Publication
    March 10, 2015
    Citations: 6
    14 miRGator Aims to be the microRNA (miRNA) portal encompassing microRNA diversity, expression profiles, target relationships, and various supporting tools. By keeping datasets and analytic tools up-to-date, miRGator should continue to serve as an integrated resource for biogenesis and functional investigation of miRNAs. /
  • human
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    Nov. 27, 2012
    Citations: 35
    15 miRNet miRNet is an easy-to-use web-based tool with comprehensive supports for statistical analysis and functional interpretation of various datasets generated in miRNAs studies. Users can explore the results in miRNA-target interaction networks with powerful features to assist in biological understanding. /
  • other animals (selectable)
  • mouse
  • fish
  • worm
  • rat
  • fly
  • human
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    April 21, 2016
    Citations: 13
    16 miRSystem A database which integrates seven well known miRNA target gene prediction programs: DIANA, miRanda, miRBridge, PicTar, PITA, rna22, and TargetScan. This database contains validated data from TarBase and miRecords on interaction between miRNA and its target genes. /
  • human
  • mouse
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • Homepage

    Publication
    Aug. 1, 2012
    Citations: 61
    17 miRTar miRTar, which adopts seven scenarios to identify putative miRNA target sites of the gene transcripts and elucidates the biological functions of miRNAs toward their targets in metabolic pathways. The prediction system considers seven scenarios (one miRNA to one gene, one miRNA to N genes, N miRNAs to one gene, N miRNAs to M genes, all miRNAs to N genes and N miRNAs to metabolic pathways) to help biologists to identify easily the regulatory relationships between interesting miRNAs and their targets, not only in 3'UTR but also in 5'UTR and coding regions. /
  • human
  • KEGG Pathways
  • Homepage

    Publication
    July 26, 2011
    Citations: 32
    18 mirTools 2.0 MirTools 2.0 is updated version of mirTools, which was developed to comprehensive characterize the small RNA transcriptome obtained from high-throughput sequencing. It enables user to: detect and profile non-coding RNA (tRNA, snRNA, snoRNA, rRNA ans piRNA); obtain detailed annotation ifmromation about known miRNA (absolute/realtive reds count and most abundant tags); identify the microRNA targeted genes and their detailed functional annotate; perform the comparison of many samples and identify the differentially expressed non-coding RNAs between experimental groups; discovery the novel miRNAs. /
  • human
  • mouse
  • rat
  • chicken
  • fish
  • worm
  • fly
  • other animals (selectable)
  • plants (selectable)
  • any (local)
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • Homepage

    Publication
    May 29, 2013
    Citations: 25
    19 miTALOS v2 miTALOS v2 is a user-friendly web application to identify pathways regulated by miRNAs in a tissue specific manner. With miTALOS v2 users can analyze multiple miRNAs together to account for combinatorial effects. /
  • human
  • mouse
  • KEGG Pathways
  • Protein-Protein Interaction
  • Homepage

    Publication
    March 21, 2016
    Citations: 9
    20 MMIA MMIA integrates microRNA and mRNA expression data with predicted microRNA target information for analyzing microRNA-associated phenotypes and biological functions by Gene Set Enrichment Analysis. To assign biological relevance to the integrated microRNA/mRNA profiles, MMIA uses exhaustive human genome coverage, including various disease-associated genes as well as conventional canonical pathways and Gene Ontology. This novel web server provides users with miRNA-mRNA expression data combined analysis tools and broad gene sets. /
  • human
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    May 6, 2009
    Citations: 71
    21 MTide MTide is an integrated pipeline designed to parse sRNA-seq and degradome data for miRNA-target identification in plant. It can quantify the known miRNA expression and identify novel miRNA from sRNA-seq data, identify the target of miRNA from degradome data signature, predict target of miRNA precisely, prioritize predicted target according to GO similarity to known or validated target, and identify the expressed miRNA between two samples. /
  • plants
  • GO Terms
  • Homepage

    Publication
    Sept. 24, 2014
    Citations: 14
    22 Oasis 2.0 Oasis is a web application that allows for the fast and flexible online analysis of small-RNA-seq (sRNA-seq) data. Oasis’ exclusive selling points are a differential expression module that allows for the multivariate analysis of samples, a classification module for robust biomarker detection and an advanced programming interface that supports the batch submission of jobs. Both modules include the analysis of novel miRNAs, miRNA targets and functional analyses including GO and pathway enrichment. /
  • human
  • mouse
  • fly
  • fish
  • worm
  • chicken
  • rat
  • other animals (selectable)
  • GO Terms
  • KEGG Pathways
  • Protein-Protein Interaction
  • Homepage

    Publication
    Feb. 19, 2015
    Citations: 16
    23 PPImiRFS PPImiRFS, a novel method to obtain the functional similarity scores of plant miRNA pairs based on a PPIN with semantic similarity weights generated using GO terms and graph theoretic properties. /
  • plants
  • Functional Similarity
  • Homepage

    Publication
    Nov. 4, 2015
    Citations: 2
    24 sRNAtoolbox sRNAtoolbox is aimed to provide small RNA researchers with several useful tools including sRNA expression profiling from deep sequencing experiments and several downstream analysis tools. The center piece of sRNAtoolbox is sRNAbench, which allows the expression profiling and prediction of novel microRNAs in deep sequencing experiments. The other tools can be either launched on sRNAbench results, or independently using the appropriate file formats. /
  • human
  • mouse
  • rat
  • chicken
  • fly
  • fish
  • viruses
  • plants (selectable)
  • bacteria
  • other animals (selectable)
  • GO Terms
  • Homepage

    Publication
    May 27, 2015
    Citations: 38
    25 TaLasso TaLasso algorithm combines the information of sequence databases with mRNA and miRNA expression to quantify the down-regulation between miRNAs and their putative targets. /
  • human
  • miRNA/mRNA Correlation
  • Homepage

    Publication
    Feb. 14, 2012
    Citations: 21
    26 wapRNA wapRNA provides an integrated tool for RNA sequence, refers to the use of High-throughput sequencing technologies to sequence cDNAs in order to get information about a sample's RNA content. wapRNA provides researchers with efficient ways to measure RNA sequence experimentally, allowing them to get information such as how different alleles of a gene are expressed, detect post-transcriptional mutations or identifying gene fusions, annotate the known miRNAs or predict the news and so on.  /
  • human
  • mouse
  • rat
  • worm
  • fly
  • chicken
  • worm
  • fish
  • other animals (selectable)
  • any (local)
  • GO Terms
  • KEGG Pathways
  • Homepage

    Publication
    Sept. 6, 2011
    Citations: 23